Exam 1

structure of an amino acid

structure of an amino acid

1. amino functional group

2. carboxylic acid

3. hydrogen atom

4. a variable side chain

When the side chain in an amino acid has a negative charge

It has lost a proton and is acidic

When the side chain in an amino acid has a positive charge

It has taken a proton and is basic

When the side chain in an amino acid is uncharged but has an oxygen atom

The highly electronegative oxygen will result in a polar covalent bond and thus is uncharged polar

When the side chain in an amino acid is uncharged and does not have an oxygen

The side change is non-polar and hydrophobic

When atoms of different electronegativites are bonded together, they form molecules that are:

polar, charged, water-soluble, and reactive

condensation reaction

monomer in, water out

hydrolysis

water in, monomer out

peptide bond

the bond formed between the carboxylic acid of one amino acid and the amino group of another amino acid. condensation reaction

properties of a polypeptide chain

flexible, has directionality, and its side chains extend out from the peptide-bonded backbone

Protein primary structure

the unique sequence of amino acids held together by peptide bonds

How can just a single amino acid change radically alter a protein’s function?

Each amino acid’s R group affects a polypeptide’s size, shape, chemical reactivity, and interaction with water.

Ex: sickle cell disease is caused by a single change in the amino acid sequence

protein secondary structure

formed by hydrogen bonds between the carbonyl group of one amino acid and the amino group of another

the two types of protein secondary structure

alpha-helices and beta-pleated sheets

Protein tertiary structure

interactions between R-groups or between R-groups and the peptide backbone

causes polypeptide to fold into 3D shape

Protein quaternary structure

the bonding of two or more polypeptide subunits

Why is protein folding spontaneous?

The hydrogen bonds and Van der Waal interactions make the folded protein more stable energetically than unfolded molecules

Denatured protein

an unfolded protein that is not able to function normally

molecular chaperons

proteins that help other proteins fold correctly

ex: they will bind to non-polar sections of a polypeptide chain to prohibit hydrophobic interactions

The purpose of DNA and RNA

-storage and transmission of genetic info

-structural and catalytic roles

nucleic acid

a polymer of nucleotides

what is a nucleotide composed of?

A phosphate group, a sugar, and a nitrogenous base

Which Carbon is the Phosphate attached to in a nucleic acid?

5’

ribose

sugar in ribonucleotides (RNA)

-OH on 2’ carbon

deoxyribose

sugar in deoxynucleotides (DNA)

-H on 2’ carbon

Purines

- adenine (A) and guanine (G)

-have two rings

Pyrimidines

-cytocine (C), uracil (U), and Thymine (T)

-have one ring

Where on the 5’ carbon is the nitrogenous base linked?

1’ carbon

how are DNA strands read ?

Starting with the 5’ phosphate group and ending with the 3’ hydroxyl group

phosphodiester bond

-links two nucleotides together

-a condensation reaction occurs between the 5’ phosphate group and the 3’ OH group on a neighboring nucleotide

Nucleoside

sugar base only, no phosphate group

Chargaff’s rule

# of purines = # of pyrimidines

Rosalind Franklin’s key discovery

DNA molecules form a helix with a repeating structure

What is the regular repeating pattern in DNA?

.34 nm, 2.0 nm, and 3.4 nm

how does base stacking contribute to DNA stability?

the non polar, flat surfaces of the bases stacking tightly as possible with one another causes them to group together away from water molecules

How many h bonds are in the G-C pairing?

3

How many h bonds are in the A-T pairing?

2

what do the nitrogenous bases contain?

genetic code

DNA primary structure

sequence of deoxyribonucleotides; bases are A, T, G, and C

DNA secondary structure

Two antiparallel strands twist into a double helix, stabilized by hydrogen bonding between complementary base pairs (A-T, C-G) and hydrophobic interactions

DNA tertiary structure

Double helix forms compact structures by twisting into supercoils or wrapping around proteins

RNA primary structure

Sequence of ribonucleotides; bases are A, U, G, and C

RNA secondary structure

Most common are hairpins, formed when a single strand folds back on itself to form a double helix “stem” and an unpaired “loop”

RNA tertiary structure

Secondary structures fold to form a wide variety of distinctive 3D shapes

Carbohydrate

“hydrated carbon”

Simple carbs

• Digest quickly; high glycemic index

• spike blood glucose levels

• vitamin and mineral rich in fruit

• otherwise are found in processed foods

• do not produce feeling of fullness

complex carbs

• Digest slowly; low glycemic index

• do not spike blood glucose levels

• vitamin and mineral rich

• good for digestive health

• keep body satiated (full)

Aldehyde sugar (aldose)

have the carbonyl group at the end of the molecule

Ketone sugar (ketose)

have the carbonyl group in the middle of the carbon chain

Isomers

same chemical formula but different structures

Glycosidic linkage

condensation reaction between the hydroxyl groups on two monosaccharides

Starch

• plant energy storage

• mix of amylose and amylopectin

• branches when an alpha-1,4-glycosidic linkage forms between monomers on two strands (1 in 30 glucose molecules)

Glycogen

• Animal energy storage

• alpha-1,4-glycosidic linkage

• very similar to amylopectin starch, except more branches (1 in 10 glucose molecules)

Cellulose

• Major component of plant cell walls

• beta-glucose monomers

• linear strands (not helical)

• forms long, parallel strands held together by H bonds

Chitin

• Structural support for fungi cell walls, component of insect and crustacean cytoskeleton

• monomers = N-acetyl glucosamine

• NAc subunits form H bonds between adjacent strands—> results in tough, stiff sheet for protection

• Can be combined with calcium carbonate as in exoskeleton of crustacea or with sclerotin in arthropods

Peptidoglycan

• Structural support of bacterial cell wall

• Complex — long backbone, with 2 types of alternating monosaccharides, beta-1,4-gycosidic linkages

• peptide bonds form between amino acids of adjacent strands

How does penicillin work?

It binds tightly to enzymes that catalyze the formation of cross-link between individual strands within peptidoglycan. This causes the cell wall to weaken and break.

Amylase

catalyzes the hydrolysis of alpha-glycosidic linkages in starch

phosphorylase

catalyzes the hydrolysis of alpha-glycosidic linkages in glycogen

Plasma membrane

layer of molecules, mostly lipids, that surrounds the cell. Regulates the passage of molecules and ions in and out the cell

Selective barrier

prevent entry of harmful molecules and facilitate entry of necessary molecules

components of a lipid

major hydrocarbon component and are mostly nonpolar and hydrophobic

lipids are defined by their…

solubility

structure and function of steroids

• 4-ring structure

• bulky

• amphipathic—> polar head and non polar tails

• Function:

  • cell signaling —> hormones: estrogen and testosterone

  • plasma membrane component—> cholesterol

Saturated fatty acid

• solid at room temperature

• ex) butter

• not good for your health

• every carbon has the max amount of hydrogen molecules

Unsaturated fatty acids

• liquid at room temperature

• ex) oils

• not all carbons have the max amount of hydrogen atoms attached

• C=C gives the tail a kink

Structure and function of fats

• 3 fatty acids linked to glycerol (aka triglyceride)

  • Ester linkage

• Lipids do not create a polymer

• Function: energy storage

Ester linkage

condensation reaction between the OH on glycerol and the carboxyl on the fatty acid

Structure and function of a phospholipid

• 2 C-H chains and a phosphate group linked to glycerol

• Function

  • cell membrane component

• Amphipathic—> has a polar/hydrophilic head and a non-polar/hydrophobic tails

lipids in aqueous solutions will spontaneously form what?

Micelles or bilayers

Micelles

fatty acids, simple lipids (one fatty acid chain)

Lipid bilayer/ liposome

phospholipids (two fatty acid chains)

What can move across the lipid bilayer easily?

small, non-polar, and uncharged polar molecules

What can not move across the lipid bilayer easily, if at all?

Charged or large polar molecules

Why is membrane permeability critical to life?

Allows differences between internal and external environments

What factors affect membrane permeability?

1. Lipid structure

   -Bond saturation

   -Hydrocarbon length

2. Cholesterol content in membrane

3. Temperature

How does lipid structure affect permeability?

Bilayers with unsaturated hydrocarbons and/or shorter hydrocarbon tails are more fluid and permeable than those with saturated hydrocarbons and/or longer tails

the more unsaturated fats in bilayer = more permeable

Cholesterol

component of animal cell membranes, amphipathic

How does cholesterol affect the fluidity of a cell membrane?

At normal cell temperatures, the interaction of the rigid structure of cholesterol with the phospholipid fatty acid tails reduces the mobility of the phospholipids and the fluidity of the membrane.

Cholesterol causes a tighter packing of hydrophobic tails, reduces permeability.

More cholesterol = less permeable

How does temperature affect cell membrane fluidity?

At higher temperatures, the phospholipids have more KE which makes the membrane more fluid and permeable. At lower temperature, the phospholipids have less KE which makes the membrane less fluid and permeable.

Predictions of the Fluid Mosaic model

1. Biomolecular sheet of 2 monolayers of lipids with hydrophobic chains facing the interior and polar head groups exposed to exterior aqueous solution

2. Mobility of lipids (fluidity) is allowed only lateral and rotational, never flip-flop on monolayer to the other

3. Bilayers are asymmetric in nature

4. Membrane proteins are either integral or peripheral in nature

Receptor proteins

allow cell to receive signals from environment

Enzymes

catalyze chemical reactions

Anchor proteins

attach to other proteins that help maintain cell structure and shape

Integral proteins

Permanently associated with cell membranes and cannot be separated from the membrane experimentally without destroying it.

Threaded through bilayer and goes from one end to the other.

transmembrane protein

Type of integral protein that spans the entire lipid bilayer

Why are integral proteins amphipathic.

Remember like hangs out with like. There is a stretch of non-polar amino acids in the middle so the protein can integrate into the membrane.

3 domains of an integral protein

extracellular (polar), transmembrane (non-polar), and cytosolic (polar)

Peripheral proteins

Temporarily associated with the lipid bilayer or with integral proteins through weak non-covalent interactions.

Can be on the internal or external side of cell membrane.

Do not go through bilayer

Purpose of carbohydrates located on the outer surface of the cell membrane

• signaling/ cell-cell recognition

• Cell identification

• Attachment

• Protection

solutes

• small molecules or ions in a solution

• have thermal energy (movement)

• are in constant, random motion

Diffusion

The movement of molecules or ions across the phospholipid bilayer from an area of higher concentration to an area of lower concentration to achieve equilibrium.

“Down the concentration gradient”

Osmosis

• occurs when solutions of different concentrations are separated by a membrane is that is permeable to water but not the solutes (too big or too charged)

• Water spontaneously moves across the membrane toward the solution with the higher solute and the lower water concentration

• Dilutes the solutes with water to create equilibrium

Hypertonic solution

The solute concentration outside the cell is greater than the solute concentration inside the cell.

[out] > [in]

water will flow outside the cell

Hypotonic solution

The solute concentration outside the cell is less than the solute concentration inside the cell.

[out] < [in]

water will flow inside the cell

Isotonic solution

The solute concentration outside the cell is equal to the solute concentration inside the cell.

[out] = [in]

In a hypertonic solution…

water will move out of the cell by osmosis = cell shrinks

In a hypotonic solution…

water will move into the cell by osmosis = cell swells

In an isotonic solution…

There will be no net water movement = cell remains same size

Passive transport

does not require an input of energy, can be simple diffusion or protein facilitated diffusion; the direction of flow occurs down a concentration gradient